Go ahead and scrape it clean when you find something that died
That smell is indeed ammonia but you are handling this rock like dentistry, that's tooth decay zone and you debride it clean back to clean under rock/ rinse and get the rotting flesh portion out
It's all external work where you are setting the rock on the counter vs messing with the water column.
Scrape clean. Rinse out with saltwater so no smell meat remains
These are hidden hitchhikers that may die or live, be active when hand guiding is needed. When that rock was in the ocean, things attached to it that an aquarium might not keep well. It won't take long for things to balance out, keep inspecting it, lift a piece out and check it over as it matures since it's new to your tank and fresh out of shipping.
Any dead zones, knife it back to rock and remove flesh dying and rinse away. Based on your prior pics there's not tons of things to die. An associated clam isn't uncommon, I barely had mine die after 4 years good lifespan bc my heater failed and temps dropped. I cleaned it out and put the cool shell back in. Active
Also on your prior thread we talked about a good % water change needed to be ran today, it's required as you are anticipating these minor curing events. In our cycling thread linked for you, it showed that we make water changes commonly at the start when fresh ocean rock is used. We are anticipating a curing phase and matching water change work per that section of the thread.
